The changes in the age-standardised incidence rates (ASIR) of cancer from 1990–1994 to 1995–1999 were studied, based on the Estonian Cancer Registry’s data. For all cancer sites together, the ASIR increased 6% in males and 11% in females. The most significant rise in the ASIR was observed for thyroid cancer in females (74%), and for non-Hodgkin’s lymphoma and for malignant skin melanoma both in males (44% and 42%, respectively) and females (59% and 44%, respectively). A significant increase was revealed also for cancers of the brain and other parts of central nervous system, kidney, skin (non-melanoma), urinary bladder, prostate, rectum and colon in males, and for cancers of the skin (non-melanoma), urinary bladder, breast and colon in females. A decrease was observed in the incidence of leukaemia and stomach cancer. The ASIR decreased also for cancers of oesophagus, larynx, lung and liver in males, and for cancers of the pancreas and ovary in females. The levelling out of the incidence rates for lung cancer in males can be regarded as the most notable change, which evidently reflects a longterm shift in male smoking habits. The continuously high incidence of invasive cervical cancer primarily indicates the lack of an organised mass screening programme in Estonia.